Hawkeye is one of SHIELD's top agents. They're not going to kick him out just because he got mind-controlled by a God wielding a mystical McGuffin spear that NO ONE outside of Thor was prepared for or knew how to handle. Gods and aliens are outside of his skill set, at least back then. Plus, SHIELD isn't exactly a squeaky clean organization period, so I doubt that there going to hold it against Hawkeye. They brought Black Widow in and she was an out and out villain in the past after all.